Cantera  2.3.0
Kinetics Class Reference

Public interface for kinetics managers. More...

#include <Kinetics.h>

Inheritance diagram for Kinetics:
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Collaboration diagram for Kinetics:
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## Public Member Functions

Returns true if the kinetics manager has been properly initialized and finalized. More...

virtual std::pair< size_t, size_t > checkDuplicates (bool throw_err=true) const
Check for duplicate reactions. More...

void selectPhase (const doublereal *data, const thermo_t *phase, doublereal *phase_data)

Constructors and General Information about Mechanism
Kinetics ()
Default constructor. More...

virtual ~Kinetics ()

Kinetics (const Kinetics &)

Kineticsoperator= (const Kinetics &right)

virtual KineticsduplMyselfAsKinetics (const std::vector< thermo_t *> &tpVector) const
Duplication routine for objects which inherit from Kinetics. More...

virtual void assignShallowPointers (const std::vector< thermo_t *> &tpVector)
Reassign the pointers within the Kinetics object. More...

virtual int type () const
Identifies the kinetics manager type. More...

virtual std::string kineticsType () const
Identifies the Kinetics manager type. More...

size_t nReactions () const
Number of reactions in the reaction mechanism. More...

void checkReactionIndex (size_t m) const
Check that the specified reaction index is in range Throws an exception if i is greater than nReactions() More...

void checkReactionArraySize (size_t ii) const
Check that an array size is at least nReactions() Throws an exception if ii is less than nReactions(). More...

void checkSpeciesIndex (size_t k) const
Check that the specified species index is in range Throws an exception if k is greater than nSpecies()-1. More...

void checkSpeciesArraySize (size_t mm) const
Check that an array size is at least nSpecies() Throws an exception if kk is less than nSpecies(). More...

Information/Lookup Functions about Phases and Species
size_t nPhases () const
The number of phases participating in the reaction mechanism. More...

void checkPhaseIndex (size_t m) const
Check that the specified phase index is in range Throws an exception if m is greater than nPhases() More...

void checkPhaseArraySize (size_t mm) const
Check that an array size is at least nPhases() Throws an exception if mm is less than nPhases(). More...

size_t phaseIndex (const std::string &ph)
Return the phase index of a phase in the list of phases defined within the object. More...

size_t surfacePhaseIndex ()
This returns the integer index of the phase which has ThermoPhase type cSurf. More...

size_t reactionPhaseIndex ()
Phase where the reactions occur. More...

thermo_tthermo (size_t n=0)
This method returns a reference to the nth ThermoPhase object defined in this kinetics mechanism. More...

const thermo_tthermo (size_t n=0) const

size_t nTotalSpecies () const
The total number of species in all phases participating in the kinetics mechanism. More...

size_t kineticsSpeciesIndex (size_t k, size_t n) const
The location of species k of phase n in species arrays. More...

std::string kineticsSpeciesName (size_t k) const
Return the name of the kth species in the kinetics manager. More...

size_t kineticsSpeciesIndex (const std::string &nm) const
This routine will look up a species number based on the input std::string nm. More...

size_t kineticsSpeciesIndex (const std::string &nm, const std::string &ph) const
This routine will look up a species number based on the input std::string nm. More...

thermo_tspeciesPhase (const std::string &nm)
This function looks up the name of a species and returns a reference to the ThermoPhase object of the phase where the species resides. More...

thermo_tspeciesPhase (size_t k)
This function takes as an argument the kineticsSpecies index (i.e., the list index in the list of species in the kinetics manager) and returns the species' owning ThermoPhase object. More...

size_t speciesPhaseIndex (size_t k)
This function takes as an argument the kineticsSpecies index (i.e., the list index in the list of species in the kinetics manager) and returns the index of the phase owning the species. More...

Reaction Rates Of Progress
virtual void getFwdRatesOfProgress (doublereal *fwdROP)
Return the forward rates of progress of the reactions. More...

virtual void getRevRatesOfProgress (doublereal *revROP)
Return the Reverse rates of progress of the reactions. More...

virtual void getNetRatesOfProgress (doublereal *netROP)
Net rates of progress. More...

virtual void getEquilibriumConstants (doublereal *kc)
Return a vector of Equilibrium constants. More...

virtual void getReactionDelta (const doublereal *property, doublereal *deltaProperty)
Change in species properties. More...

virtual void getRevReactionDelta (const doublereal *g, doublereal *dg)
Given an array of species properties 'g', return in array 'dg' the change in this quantity in the reversible reactions. More...

virtual void getDeltaGibbs (doublereal *deltaG)
Return the vector of values for the reaction Gibbs free energy change. More...

virtual void getDeltaElectrochemPotentials (doublereal *deltaM)
Return the vector of values for the reaction electrochemical free energy change. More...

virtual void getDeltaEnthalpy (doublereal *deltaH)
Return the vector of values for the reactions change in enthalpy. More...

virtual void getDeltaEntropy (doublereal *deltaS)
Return the vector of values for the reactions change in entropy. More...

virtual void getDeltaSSGibbs (doublereal *deltaG)
Return the vector of values for the reaction standard state Gibbs free energy change. More...

virtual void getDeltaSSEnthalpy (doublereal *deltaH)
Return the vector of values for the change in the standard state enthalpies of reaction. More...

virtual void getDeltaSSEntropy (doublereal *deltaS)
Return the vector of values for the change in the standard state entropies for each reaction. More...

Species Production Rates
virtual void getCreationRates (doublereal *cdot)
Species creation rates [kmol/m^3/s or kmol/m^2/s]. More...

virtual void getDestructionRates (doublereal *ddot)
Species destruction rates [kmol/m^3/s or kmol/m^2/s]. More...

virtual void getNetProductionRates (doublereal *wdot)
Species net production rates [kmol/m^3/s or kmol/m^2/s]. More...

Reaction Mechanism Informational Query Routines
virtual double reactantStoichCoeff (size_t k, size_t i) const
Stoichiometric coefficient of species k as a reactant in reaction i. More...

virtual double productStoichCoeff (size_t k, size_t i) const
Stoichiometric coefficient of species k as a product in reaction i. More...

virtual doublereal reactantOrder (size_t k, size_t i) const
Reactant order of species k in reaction i. More...

virtual doublereal productOrder (int k, int i) const
product Order of species k in reaction i. More...

virtual void getActivityConcentrations (doublereal *const conc)
Get the vector of activity concentrations used in the kinetics object. More...

virtual int reactionType (size_t i) const
Flag specifying the type of reaction. More...

virtual bool isReversible (size_t i)
True if reaction i has been declared to be reversible. More...

std::string reactionString (size_t i) const
Return a string representing the reaction. More...

std::string reactantString (size_t i) const
Returns a string containing the reactants side of the reaction equation. More...

std::string productString (size_t i) const
Returns a string containing the products side of the reaction equation. More...

virtual void getFwdRateConstants (doublereal *kfwd)
Return the forward rate constants. More...

virtual void getRevRateConstants (doublereal *krev, bool doIrreversible=false)
Return the reverse rate constants. More...

Reaction Mechanism Construction
Add a phase to the kinetics manager object. More...

virtual void init ()
Prepare the class for the addition of reactions, after all phases have been added. More...

virtual void resizeSpecies ()
Resize arrays with sizes that depend on the total number of species. More...

virtual void finalize ()
Finish adding reactions and prepare for use. More...

virtual bool addReaction (shared_ptr< Reaction > r)
Add a single reaction to the mechanism. More...

virtual void modifyReaction (size_t i, shared_ptr< Reaction > rNew)
Modify the rate expression associated with a reaction. More...

shared_ptr< Reactionreaction (size_t i)
Return the Reaction object for reaction i. More...

shared_ptr< const Reactionreaction (size_t i) const

void skipUndeclaredSpecies (bool skip)
Determine behavior when adding a new reaction that contains species not defined in any of the phases associated with this kinetics manager. More...

void skipUndeclaredThirdBodies (bool skip)
Determine behavior when adding a new reaction that contains third-body efficiencies for species not defined in any of the phases associated with this kinetics manager. More...

Altering Reaction Rates
doublereal multiplier (size_t i) const
The current value of the multiplier for reaction i. More...

virtual void setMultiplier (size_t i, doublereal f)
Set the multiplier for reaction i to f. More...

virtual void invalidateCache ()

## Protected Member Functions

virtual void updateROP ()

double checkDuplicateStoich (std::map< int, double > &r1, std::map< int, double > &r2) const
Check whether r1 and r2 represent duplicate stoichiometries This function returns a ratio if two reactions are duplicates of one another, and 0.0 otherwise. More...

void checkReactionBalance (const Reaction &R)
Check that the specified reaction is balanced (same number of atoms for each element in the reactants and products). More...

## Protected Attributes

ValueCache m_cache
Cache for saved calculations within each Kinetics object. More...

size_t m_kk
The number of species in all of the phases that participate in this kinetics mechanism. More...

vector_fp m_perturb
Vector of perturbation factors for each reaction's rate of progress vector. More...

std::vector< shared_ptr< Reaction > > m_reactions
Vector of Reaction objects represented by this Kinetics manager. More...

std::vector< thermo_t * > m_thermo
m_thermo is a vector of pointers to ThermoPhase objects that are involved with this kinetics operator More...

std::vector< size_t > m_start
m_start is a vector of integers specifying the beginning position for the species vector for the n'th phase in the kinetics class. More...

std::map< std::string, size_t > m_phaseindex
Mapping of the phase id, i.e., the id attribute in the XML phase element to the position of the phase within the kinetics object. More...

size_t m_surfphase
Index in the list of phases of the one surface phase. More...

size_t m_rxnphase
Phase Index where reactions are assumed to be taking place. More...

size_t m_mindim
number of spatial dimensions of lowest-dimensional phase. More...

vector_fp m_rfn
Forward rate constant for each reaction. More...

vector_fp m_rkcn
Reciprocal of the equilibrium constant in concentration units. More...

vector_fp m_ropf
Forward rate-of-progress for each reaction. More...

vector_fp m_ropr
Reverse rate-of-progress for each reaction. More...

vector_fp m_ropnet
Net rate-of-progress for each reaction. More...

bool m_skipUndeclaredSpecies

bool m_skipUndeclaredThirdBodies

Stoichiometry management
StoichManagerN m_reactantStoich
Stoichiometry manager for the reactants for each reaction. More...

StoichManagerN m_revProductStoich
Stoichiometry manager for the products of reversible reactions. More...

StoichManagerN m_irrevProductStoich
Stoichiometry manager for the products of irreversible reactions. More...

## Detailed Description

Public interface for kinetics managers.

This class serves as a base class to derive 'kinetics managers', which are classes that manage homogeneous chemistry within one phase, or heterogeneous chemistry at one interface. The virtual methods of this class are meant to be overloaded in subclasses. The non-virtual methods perform generic functions and are implemented in Kinetics. They should not be overloaded. Only those methods required by a subclass need to be overloaded; the rest will throw exceptions if called.

When the nomenclature "kinetics species index" is used below, this means that the species index ranges over all species in all phases handled by the kinetics manager.

Definition at line 111 of file Kinetics.h.

## ◆ Kinetics() [1/2]

 Kinetics ( )

Default constructor.

Definition at line 20 of file Kinetics.cpp.

## ◆ Kinetics() [2/2]

 Kinetics ( const Kinetics & right )
Deprecated:
Copy constructor to be removed after Cantera 2.3 for all classes derived from Kinetics.

Definition at line 33 of file Kinetics.cpp.

References Cantera::warn_deprecated().

## ◆ operator=()

 Kinetics & operator= ( const Kinetics & right )
Deprecated:
Assignment operator to be removed after Cantera 2.3 for all classes derived from Kinetics.

Definition at line 41 of file Kinetics.cpp.

 Kinetics * duplMyselfAsKinetics ( const std::vector< thermo_t *> & tpVector ) const
virtual

Duplication routine for objects which inherit from Kinetics.

This function can be used to duplicate objects derived from Kinetics even if the application only has a pointer to Kinetics to work with.

These routines are basically wrappers around the derived copy constructor.

Parameters
 tpVector Vector of pointers to ThermoPhase objects. this is the m_thermo vector within this object
Deprecated:
To be removed after Cantera 2.3 for all classes derived from Kinetics.

Reimplemented in InterfaceKinetics, AqueousKinetics, EdgeKinetics, GasKinetics, and BulkKinetics.

Definition at line 72 of file Kinetics.cpp.

## ◆ assignShallowPointers()

 void assignShallowPointers ( const std::vector< thermo_t *> & tpVector )
virtual

Reassign the pointers within the Kinetics object.

This type or routine is necessary because the Kinetics object doesn't own the ThermoPhase objects. After a duplication, we need to point to different ThermoPhase objects.

We check that the ThermoPhase objects are aligned in the same order and have the following identical properties to the ones that they are replacing:

Parameters
 tpVector Vector of pointers to ThermoPhase objects. this is the m_thermo vector within this object
Deprecated:
To be removed after Cantera 2.3 for all classes derived from Kinetics.

Definition at line 129 of file Kinetics.cpp.

References Phase::id(), Kinetics::m_thermo, Phase::nSpecies(), and ThermoPhase::type().

## ◆ type()

 int type ( ) const
virtual

Identifies the kinetics manager type.

Each class derived from Kinetics should overload this method to return a unique integer. Standard values are defined in file mix_defs.h.

Deprecated:
Use kineticsType() instead. To be removed after Cantera 2.3.

Reimplemented in InterfaceKinetics, AqueousKinetics, EdgeKinetics, and GasKinetics.

Definition at line 81 of file Kinetics.cpp.

References Cantera::warn_deprecated().

## ◆ kineticsType()

 virtual std::string kineticsType ( ) const
inlinevirtual

Identifies the Kinetics manager type.

Each class derived from Kinetics should override this method to return a meaningful identifier.

Reimplemented in InterfaceKinetics, AqueousKinetics, EdgeKinetics, and GasKinetics.

Definition at line 179 of file Kinetics.h.

## ◆ nReactions()

 size_t nReactions ( ) const
inline

## ◆ checkReactionIndex()

 void checkReactionIndex ( size_t m ) const

Check that the specified reaction index is in range Throws an exception if i is greater than nReactions()

Definition at line 87 of file Kinetics.cpp.

References Kinetics::nReactions().

Referenced by Kinetics::modifyReaction(), and Kinetics::reaction().

## ◆ checkReactionArraySize()

 void checkReactionArraySize ( size_t ii ) const

Check that an array size is at least nReactions() Throws an exception if ii is less than nReactions().

Used before calls which take an array pointer.

Definition at line 94 of file Kinetics.cpp.

References Kinetics::nReactions().

## ◆ checkSpeciesIndex()

 void checkSpeciesIndex ( size_t k ) const

Check that the specified species index is in range Throws an exception if k is greater than nSpecies()-1.

Definition at line 115 of file Kinetics.cpp.

References Kinetics::m_kk.

## ◆ checkSpeciesArraySize()

 void checkSpeciesArraySize ( size_t mm ) const

Check that an array size is at least nSpecies() Throws an exception if kk is less than nSpecies().

Used before calls which take an array pointer.

Definition at line 122 of file Kinetics.cpp.

References Kinetics::m_kk.

## ◆ nPhases()

 size_t nPhases ( ) const
inline

The number of phases participating in the reaction mechanism.

For a homogeneous reaction mechanism, this will always return 1, but for a heterogeneous mechanism it will return the total number of phases in the mechanism.

Definition at line 216 of file Kinetics.h.

References Kinetics::m_thermo.

## ◆ checkPhaseIndex()

 void checkPhaseIndex ( size_t m ) const

Check that the specified phase index is in range Throws an exception if m is greater than nPhases()

Definition at line 101 of file Kinetics.cpp.

References Kinetics::nPhases().

## ◆ checkPhaseArraySize()

 void checkPhaseArraySize ( size_t mm ) const

Check that an array size is at least nPhases() Throws an exception if mm is less than nPhases().

Used before calls which take an array pointer.

Definition at line 108 of file Kinetics.cpp.

References Kinetics::nPhases().

## ◆ phaseIndex()

 size_t phaseIndex ( const std::string & ph )
inline

Return the phase index of a phase in the list of phases defined within the object.

Parameters
 ph std::string name of the phase

If a -1 is returned, then the phase is not defined in the Kinetics object.

Definition at line 238 of file Kinetics.h.

References Kinetics::m_phaseindex, and Cantera::npos.

## ◆ surfacePhaseIndex()

 size_t surfacePhaseIndex ( )
inline

This returns the integer index of the phase which has ThermoPhase type cSurf.

For heterogeneous mechanisms, this identifies the one surface phase. For homogeneous mechanisms, this returns -1.

Definition at line 251 of file Kinetics.h.

References Kinetics::m_surfphase.

Referenced by InterfaceKinetics::buildSurfaceArrhenius(), solveSP::calc_t(), and solveSP::fun_eval().

## ◆ reactionPhaseIndex()

 size_t reactionPhaseIndex ( )
inline

Phase where the reactions occur.

For heterogeneous mechanisms, one of the phases in the list of phases represents the 2D interface or 1D edge at which the reactions take place. This method returns the index of the phase with the smallest spatial dimension (1, 2, or 3) among the list of phases. If there is more than one, the index of the first one is returned. For homogeneous mechanisms, the value 0 is returned.

Definition at line 263 of file Kinetics.h.

References Kinetics::m_rxnphase.

Referenced by InterfaceKinetics::buildSurfaceArrhenius(), and InterfaceKinetics::init().

## ◆ thermo()

 thermo_t& thermo ( size_t n = 0 )
inline

This method returns a reference to the nth ThermoPhase object defined in this kinetics mechanism.

It is typically used so that member functions of the ThermoPhase object may be called. For homogeneous mechanisms, there is only one object, and this method can be called without an argument to access it.

Parameters
 n Index of the ThermoPhase being sought.

Definition at line 276 of file Kinetics.h.

References Kinetics::m_thermo.

## ◆ nTotalSpecies()

 size_t nTotalSpecies ( ) const
inline

The total number of species in all phases participating in the kinetics mechanism.

This is useful to dimension arrays for use in calls to methods that return the species production rates, for example.

Definition at line 288 of file Kinetics.h.

References Kinetics::m_kk.

## ◆ kineticsSpeciesIndex() [1/3]

 size_t kineticsSpeciesIndex ( size_t k, size_t n ) const
inline

The location of species k of phase n in species arrays.

Kinetics manager classes return species production rates in flat arrays, with the species of each phases following one another, in the order the phases were added. This method is useful to find the value for a particular species of a particular phase in arrays returned from methods like getCreationRates that return an array of species-specific quantities.

Example: suppose a heterogeneous mechanism involves three phases. The first contains 12 species, the second 26, and the third 3. Then species arrays must have size at least 41, and positions 0 - 11 are the values for the species in the first phase, positions 12 - 37 are the values for the species in the second phase, etc. Then kineticsSpeciesIndex(7, 0) = 7, kineticsSpeciesIndex(4, 1) = 16, and kineticsSpeciesIndex(2, 2) = 40.

Parameters
 k species index n phase index for the species

Definition at line 310 of file Kinetics.h.

References Kinetics::m_start.

## ◆ kineticsSpeciesName()

 string kineticsSpeciesName ( size_t k ) const

Return the name of the kth species in the kinetics manager.

k is an integer from 0 to ktot - 1, where ktot is the number of species in the kinetics manager, which is the sum of the number of species in all phases participating in the kinetics manager. If k is out of bounds, the string "<unknown>" is returned.

Parameters
 k species index

Definition at line 334 of file Kinetics.cpp.

References Kinetics::m_start, Cantera::npos, Phase::speciesName(), and Kinetics::thermo().

Referenced by Kinetics::productStoichCoeff(), and Kinetics::reactantStoichCoeff().

## ◆ kineticsSpeciesIndex() [2/3]

 size_t kineticsSpeciesIndex ( const std::string & nm ) const

This routine will look up a species number based on the input std::string nm.

The lookup of species will occur for all phases listed in the kinetics object.

return

• If a match is found, the position in the species list is returned.
• If no match is found, the value -1 is returned.
Parameters
 nm Input string name of the species

Definition at line 344 of file Kinetics.cpp.

## ◆ kineticsSpeciesIndex() [3/3]

 size_t kineticsSpeciesIndex ( const std::string & nm, const std::string & ph ) const

This routine will look up a species number based on the input std::string nm.

The lookup of species will occur in the specified phase of the object, or all phases if ph is "<any>".

return

• If a match is found, the position in the species list is returned.
• If no match is found, the value npos (-1) is returned.
Parameters
 nm Input string name of the species ph Input string name of the phase.

Definition at line 357 of file Kinetics.cpp.

## ◆ speciesPhase() [1/2]

 thermo_t & speciesPhase ( const std::string & nm )

This function looks up the name of a species and returns a reference to the ThermoPhase object of the phase where the species resides.

Will throw an error if the species doesn't match.

Parameters
 nm String containing the name of the species.

Definition at line 377 of file Kinetics.cpp.

References Kinetics::m_thermo, Cantera::npos, Phase::speciesIndex(), and Kinetics::thermo().

## ◆ speciesPhase() [2/2]

 thermo_t& speciesPhase ( size_t k )
inline

This function takes as an argument the kineticsSpecies index (i.e., the list index in the list of species in the kinetics manager) and returns the species' owning ThermoPhase object.

Parameters
 k Species index

Definition at line 369 of file Kinetics.h.

References Kinetics::speciesPhaseIndex(), and Kinetics::thermo().

## ◆ speciesPhaseIndex()

 size_t speciesPhaseIndex ( size_t k )

This function takes as an argument the kineticsSpecies index (i.e., the list index in the list of species in the kinetics manager) and returns the index of the phase owning the species.

Parameters
 k Species index

Definition at line 388 of file Kinetics.cpp.

References Kinetics::m_start, and Cantera::npos.

## ◆ getFwdRatesOfProgress()

 void getFwdRatesOfProgress ( doublereal * fwdROP )
virtual

Return the forward rates of progress of the reactions.

Forward rates of progress. Return the forward rates of progress in array fwdROP, which must be dimensioned at least as large as the total number of reactions.

Parameters
 fwdROP Output vector containing forward rates of progress of the reactions. Length: nReactions().

Definition at line 410 of file Kinetics.cpp.

References Kinetics::m_ropf.

## ◆ getRevRatesOfProgress()

 void getRevRatesOfProgress ( doublereal * revROP )
virtual

Return the Reverse rates of progress of the reactions.

Return the reverse rates of progress in array revROP, which must be dimensioned at least as large as the total number of reactions.

Parameters
 revROP Output vector containing reverse rates of progress of the reactions. Length: nReactions().

Definition at line 416 of file Kinetics.cpp.

References Kinetics::m_ropr.

## ◆ getNetRatesOfProgress()

 void getNetRatesOfProgress ( doublereal * netROP )
virtual

Net rates of progress.

Return the net (forward - reverse) rates of progress in array netROP, which must be dimensioned at least as large as the total number of reactions.

Parameters
 netROP Output vector of the net ROP. Length: nReactions().

Definition at line 422 of file Kinetics.cpp.

References Kinetics::m_ropnet.

## ◆ getEquilibriumConstants()

 virtual void getEquilibriumConstants ( doublereal * kc )
inlinevirtual

Return a vector of Equilibrium constants.

Return the equilibrium constants of the reactions in concentration units in array kc, which must be dimensioned at least as large as the total number of reactions.

$Kc_i = exp [ \Delta G_{ss,i} ] prod(Cs_k) exp(\sum_k \nu_{k,i} F \phi_n) ]$

Parameters
 kc Output vector containing the equilibrium constants. Length: nReactions().

Reimplemented in InterfaceKinetics, AqueousKinetics, and GasKinetics.

Definition at line 429 of file Kinetics.h.

Referenced by BulkKinetics::getRevRateConstants().

## ◆ getReactionDelta()

 void getReactionDelta ( const doublereal * property, doublereal * deltaProperty )
virtual

Change in species properties.

Given an array of molar species property values $$z_k, k = 1, \dots, K$$, return the array of reaction values

$\Delta Z_i = \sum_k \nu_{k,i} z_k, i = 1, \dots, I.$

For example, if this method is called with the array of standard-state molar Gibbs free energies for the species, then the values returned in array deltaProperty would be the standard-state Gibbs free energies of reaction for each reaction.

Parameters
 property Input vector of property value. Length: m_kk. deltaProperty Output vector of deltaRxn. Length: nReactions().

Definition at line 428 of file Kinetics.cpp.

## ◆ getRevReactionDelta()

 void getRevReactionDelta ( const doublereal * g, doublereal * dg )
virtual

Given an array of species properties 'g', return in array 'dg' the change in this quantity in the reversible reactions.

Array 'g' must have a length at least as great as the number of species, and array 'dg' must have a length as great as the total number of reactions. This method only computes 'dg' for the reversible reactions, and the entries of 'dg' for the irreversible reactions are unaltered. This is primarily designed for use in calculating reverse rate coefficients from thermochemistry for reversible reactions.

Definition at line 438 of file Kinetics.cpp.

## ◆ getDeltaGibbs()

 virtual void getDeltaGibbs ( doublereal * deltaG )
inlinevirtual

Return the vector of values for the reaction Gibbs free energy change.

(virtual from Kinetics.h) These values depend upon the concentration of the solution.

units = J kmol-1

Parameters
 deltaG Output vector of deltaG's for reactions Length: nReactions().

Reimplemented in InterfaceKinetics, and BulkKinetics.

Definition at line 472 of file Kinetics.h.

## ◆ getDeltaElectrochemPotentials()

 virtual void getDeltaElectrochemPotentials ( doublereal * deltaM )
inlinevirtual

Return the vector of values for the reaction electrochemical free energy change.

These values depend upon the concentration of the solution and the voltage of the phases

units = J kmol-1

Parameters
 deltaM Output vector of deltaM's for reactions Length: nReactions().

Reimplemented in InterfaceKinetics.

Definition at line 487 of file Kinetics.h.

## ◆ getDeltaEnthalpy()

 virtual void getDeltaEnthalpy ( doublereal * deltaH )
inlinevirtual

Return the vector of values for the reactions change in enthalpy.

These values depend upon the concentration of the solution.

units = J kmol-1

Parameters
 deltaH Output vector of deltaH's for reactions Length: nReactions().

Reimplemented in InterfaceKinetics, and BulkKinetics.

Definition at line 500 of file Kinetics.h.

## ◆ getDeltaEntropy()

 virtual void getDeltaEntropy ( doublereal * deltaS )
inlinevirtual

Return the vector of values for the reactions change in entropy.

These values depend upon the concentration of the solution.

units = J kmol-1 Kelvin-1

Parameters
 deltaS Output vector of deltaS's for reactions Length: nReactions().

Reimplemented in InterfaceKinetics, and BulkKinetics.

Definition at line 513 of file Kinetics.h.

## ◆ getDeltaSSGibbs()

 virtual void getDeltaSSGibbs ( doublereal * deltaG )
inlinevirtual

Return the vector of values for the reaction standard state Gibbs free energy change.

These values don't depend upon the concentration of the solution.

units = J kmol-1

Parameters
 deltaG Output vector of ss deltaG's for reactions Length: nReactions().

Reimplemented in InterfaceKinetics, and BulkKinetics.

Definition at line 527 of file Kinetics.h.

## ◆ getDeltaSSEnthalpy()

 virtual void getDeltaSSEnthalpy ( doublereal * deltaH )
inlinevirtual

Return the vector of values for the change in the standard state enthalpies of reaction.

These values don't depend upon the concentration of the solution.

units = J kmol-1

Parameters
 deltaH Output vector of ss deltaH's for reactions Length: nReactions().

Reimplemented in InterfaceKinetics, and BulkKinetics.

Definition at line 541 of file Kinetics.h.

## ◆ getDeltaSSEntropy()

 virtual void getDeltaSSEntropy ( doublereal * deltaS )
inlinevirtual

Return the vector of values for the change in the standard state entropies for each reaction.

These values don't depend upon the concentration of the solution.

units = J kmol-1 Kelvin-1

Parameters
 deltaS Output vector of ss deltaS's for reactions Length: nReactions().

Reimplemented in InterfaceKinetics, and BulkKinetics.

Definition at line 555 of file Kinetics.h.

## ◆ getCreationRates()

 void getCreationRates ( doublereal * cdot )
virtual

Species creation rates [kmol/m^3/s or kmol/m^2/s].

Return the species creation rates in array cdot, which must be dimensioned at least as large as the total number of species in all phases.

nTotalSpecies.
Parameters
 cdot Output vector of creation rates. Length: m_kk.

Definition at line 447 of file Kinetics.cpp.

## ◆ getDestructionRates()

 void getDestructionRates ( doublereal * ddot )
virtual

Species destruction rates [kmol/m^3/s or kmol/m^2/s].

Return the species destruction rates in array ddot, which must be dimensioned at least as large as the total number of species.

nTotalSpecies.
Parameters
 ddot Output vector of destruction rates. Length: m_kk.

Definition at line 462 of file Kinetics.cpp.

## ◆ getNetProductionRates()

 void getNetProductionRates ( doublereal * wdot )
virtual

Species net production rates [kmol/m^3/s or kmol/m^2/s].

Return the species net production rates (creation - destruction) in array wdot, which must be dimensioned at least as large as the total number of species.

nTotalSpecies.
Parameters
 wdot Output vector of net production rates. Length: m_kk.

Definition at line 473 of file Kinetics.cpp.

## ◆ reactantStoichCoeff()

 double reactantStoichCoeff ( size_t k, size_t i ) const
virtual

Stoichiometric coefficient of species k as a reactant in reaction i.

Parameters
 k kinetic species index i reaction index

Definition at line 398 of file Kinetics.cpp.

## ◆ productStoichCoeff()

 double productStoichCoeff ( size_t k, size_t i ) const
virtual

Stoichiometric coefficient of species k as a product in reaction i.

Parameters
 k kinetic species index i reaction index

Definition at line 404 of file Kinetics.cpp.

## ◆ reactantOrder()

 virtual doublereal reactantOrder ( size_t k, size_t i ) const
inlinevirtual

Reactant order of species k in reaction i.

This is the nominal order of the activity concentration in determining the forward rate of progress of the reaction

Parameters
 k kinetic species index i reaction index

Definition at line 618 of file Kinetics.h.

## ◆ productOrder()

 virtual doublereal productOrder ( int k, int i ) const
inlinevirtual

product Order of species k in reaction i.

This is the nominal order of the activity concentration of species k in determining the reverse rate of progress of the reaction i

For irreversible reactions, this will all be zero.

Parameters
 k kinetic species index i reaction index

Definition at line 632 of file Kinetics.h.

## ◆ getActivityConcentrations()

 virtual void getActivityConcentrations ( doublereal *const conc )
inlinevirtual

Get the vector of activity concentrations used in the kinetics object.

Parameters
 [out] conc Vector of activity concentrations. Length is equal to the number of species in the kinetics object

Reimplemented in InterfaceKinetics.

Definition at line 641 of file Kinetics.h.

## ◆ reactionType()

 virtual int reactionType ( size_t i ) const
inlinevirtual

Flag specifying the type of reaction.

The legal values and their meaning are specific to the particular kinetics manager.

Parameters
 i reaction index

Definition at line 651 of file Kinetics.h.

References Kinetics::m_reactions.

## ◆ isReversible()

 virtual bool isReversible ( size_t i )
inlinevirtual

True if reaction i has been declared to be reversible.

If isReversible(i) is false, then the reverse rate of progress for reaction i is always zero.

Parameters
 i reaction index

Reimplemented in InterfaceKinetics, and BulkKinetics.

Definition at line 662 of file Kinetics.h.

## ◆ reactionString()

 std::string reactionString ( size_t i ) const
inline

Return a string representing the reaction.

Parameters
 i reaction index

Definition at line 671 of file Kinetics.h.

References Kinetics::m_reactions.

## ◆ reactantString()

 std::string reactantString ( size_t i ) const
inline

Returns a string containing the reactants side of the reaction equation.

Definition at line 676 of file Kinetics.h.

References Kinetics::m_reactions.

## ◆ productString()

 std::string productString ( size_t i ) const
inline

Returns a string containing the products side of the reaction equation.

Definition at line 681 of file Kinetics.h.

References Kinetics::m_reactions.

## ◆ getFwdRateConstants()

 virtual void getFwdRateConstants ( doublereal * kfwd )
inlinevirtual

Return the forward rate constants.

length is the number of reactions. units depends on many issues.

Parameters
 kfwd Output vector containing the forward reaction rate constants. Length: nReactions().

Reimplemented in InterfaceKinetics, AqueousKinetics, and GasKinetics.

Definition at line 693 of file Kinetics.h.

Referenced by BulkKinetics::getRevRateConstants().

## ◆ getRevRateConstants()

 virtual void getRevRateConstants ( doublereal * krev, bool doIrreversible = false )
inlinevirtual

Return the reverse rate constants.

length is the number of reactions. units depends on many issues. Note, this routine will return rate constants for irreversible reactions if the default for doIrreversible is overridden.

Parameters
 krev Output vector of reverse rate constants. doIrreversible boolean indicating whether irreversible reactions should be included.

Reimplemented in InterfaceKinetics, and BulkKinetics.

Definition at line 708 of file Kinetics.h.

 void addPhase ( thermo_t & thermo )
virtual

Add a phase to the kinetics manager object.

This must be done before the function init() is called or before any reactions are input. The following fields are updated:

• m_start -> vector of integers, containing the starting position of the species for each phase in the kinetics mechanism.
• m_surfphase -> index of the surface phase.
• m_thermo -> vector of pointers to ThermoPhase phases that participate in the kinetics mechanism.
• m_phaseindex -> map containing the std::string id of each ThermoPhase phase as a key and the index of the phase within the kinetics manager object as the value.
Parameters
 thermo Reference to the ThermoPhase to be added.

Reimplemented in InterfaceKinetics.

Definition at line 485 of file Kinetics.cpp.

## ◆ init()

 virtual void init ( )
inlinevirtual

Prepare the class for the addition of reactions, after all phases have been added.

This method is called automatically when the first reaction is added. It needs to be called directly only in the degenerate case where there are no reactions. The base class method does nothing, but derived classes may use this to perform any initialization (allocating arrays, etc.) that requires knowing the phases.

Definition at line 743 of file Kinetics.h.

## ◆ resizeSpecies()

 void resizeSpecies ( )
virtual

Resize arrays with sizes that depend on the total number of species.

Automatically called before adding each Reaction and Phase.

Reimplemented in InterfaceKinetics, and BulkKinetics.

Definition at line 504 of file Kinetics.cpp.

References Kinetics::m_kk, Kinetics::m_start, Kinetics::m_thermo, and Kinetics::nPhases().

## ◆ finalize()

 void finalize ( )
virtual

Finish adding reactions and prepare for use.

This method is called by importKinetics() after all reactions have been entered into the mechanism and before the mechanism is used to calculate reaction rates. The base class method does nothing, but derived classes may use this to perform any initialization (allocating arrays, etc.) that must be done after the reactions are entered.

Deprecated:
No longer needed. To be removed after Cantera 2.3.

Definition at line 516 of file Kinetics.cpp.

References Cantera::warn_deprecated().

 bool addReaction ( shared_ptr< Reaction > r )
virtual

Add a single reaction to the mechanism.

Derived classes should call the base class method in addition to handling their own specialized behavior.

Parameters
 r Pointer to the Reaction object to be added.
Returns
true if the reaction is added or false if it was skipped

Reimplemented in InterfaceKinetics, AqueousKinetics, GasKinetics, and BulkKinetics.

Definition at line 522 of file Kinetics.cpp.

## ◆ modifyReaction()

 void modifyReaction ( size_t i, shared_ptr< Reaction > rNew )
virtual

Modify the rate expression associated with a reaction.

The stoichiometric equation, type of the reaction, reaction orders, third body efficiencies, reversibility, etc. must be unchanged.

Parameters
 i Index of the reaction to be modified rNew Reaction with the new rate expressions

Reimplemented in InterfaceKinetics, AqueousKinetics, and GasKinetics.

Definition at line 622 of file Kinetics.cpp.

References Kinetics::checkReactionIndex(), and Kinetics::m_reactions.

## ◆ reaction()

 shared_ptr< Reaction > reaction ( size_t i )

Return the Reaction object for reaction i.

Definition at line 647 of file Kinetics.cpp.

References Kinetics::checkReactionIndex(), and Kinetics::m_reactions.

## ◆ skipUndeclaredSpecies()

 void skipUndeclaredSpecies ( bool skip )
inline

Determine behavior when adding a new reaction that contains species not defined in any of the phases associated with this kinetics manager.

If set to true, the reaction will silently be ignored. If false, (the default) an exception will be raised.

Definition at line 792 of file Kinetics.h.

References Kinetics::m_skipUndeclaredSpecies.

Referenced by Cantera::installReactionArrays().

## ◆ skipUndeclaredThirdBodies()

 void skipUndeclaredThirdBodies ( bool skip )
inline

Determine behavior when adding a new reaction that contains third-body efficiencies for species not defined in any of the phases associated with this kinetics manager.

If set to true, the given third-body efficiency will be ignored. If false, (the default) an exception will be raised.

Definition at line 801 of file Kinetics.h.

References Kinetics::m_skipUndeclaredThirdBodies.

Referenced by Cantera::installReactionArrays().

## ◆ multiplier()

 doublereal multiplier ( size_t i ) const
inline

The current value of the multiplier for reaction i.

These methods alter reaction rates. They are designed primarily for carrying out sensitivity analysis, but may be used for any purpose requiring dynamic alteration of rate constants. For each reaction, a real-valued multiplier may be defined that multiplies the reaction rate coefficient. The multiplier may be set to zero to completely remove a reaction from the mechanism.

Parameters
 i index of the reaction

Definition at line 821 of file Kinetics.h.

References Kinetics::m_perturb.

Referenced by Reactor::applySensitivity(), and InterfaceKinetics::buildSurfaceArrhenius().

## ◆ setMultiplier()

 virtual void setMultiplier ( size_t i, doublereal f )
inlinevirtual

Set the multiplier for reaction i to f.

Parameters
 i index of the reaction f value of the multiplier.

Reimplemented in BulkKinetics.

Definition at line 830 of file Kinetics.h.

References Kinetics::m_perturb.

 virtual bool ready ( ) const
inlinevirtual

Returns true if the kinetics manager has been properly initialized and finalized.

Deprecated:
Object is always ready. To be removed after Cantera 2.3.

Reimplemented in Interface, IdealGasMix, and Edge.

Definition at line 843 of file Kinetics.h.

References Cantera::warn_deprecated().

## ◆ checkDuplicates()

 std::pair< size_t, size_t > checkDuplicates ( bool throw_err = true ) const
virtual

Check for duplicate reactions.

If throw_err is true, then an exception will be thrown if any unmarked duplicate reactions are found. Otherwise, the indices of the first pair of duplicate reactions found will be returned. If no duplicate reactions are found, returns (npos, npos).

Definition at line 154 of file Kinetics.cpp.

References Kinetics::m_reactions.

Referenced by Cantera::installReactionArrays().

## ◆ selectPhase()

 void selectPhase ( const doublereal * data, const thermo_t * phase, doublereal * phase_data )

Takes as input an array of properties for all species in the mechanism and copies those values belonging to a particular phase to the output array.

Parameters
 data Input data array. phase Pointer to one of the phase objects participating in this reaction mechanism phase_data Output array where the values for the the specified phase are to be written.

Definition at line 320 of file Kinetics.cpp.

References Kinetics::m_start, Kinetics::m_thermo, Kinetics::nPhases(), and Phase::nSpecies().

## ◆ checkReactionBalance()

 void checkReactionBalance ( const Reaction & R )
protected

Check that the specified reaction is balanced (same number of atoms for each element in the reactants and products).

Raises an exception if the reaction is not balanced.

Definition at line 279 of file Kinetics.cpp.

## ◆ m_cache

 ValueCache m_cache
protected

Cache for saved calculations within each Kinetics object.

Definition at line 873 of file Kinetics.h.

## ◆ m_reactantStoich

 StoichManagerN m_reactantStoich
protected

Stoichiometry manager for the reactants for each reaction.

These objects and functions handle turning reaction extents into species production rates and also handle turning thermo properties into reaction thermo properties.

Definition at line 910 of file Kinetics.h.

## ◆ m_revProductStoich

 StoichManagerN m_revProductStoich
protected

Stoichiometry manager for the products of reversible reactions.

Definition at line 913 of file Kinetics.h.

## ◆ m_irrevProductStoich

 StoichManagerN m_irrevProductStoich
protected

Stoichiometry manager for the products of irreversible reactions.

Definition at line 916 of file Kinetics.h.

## ◆ m_kk

 size_t m_kk
protected

The number of species in all of the phases that participate in this kinetics mechanism.

Definition at line 921 of file Kinetics.h.

## ◆ m_perturb

 vector_fp m_perturb
protected

Vector of perturbation factors for each reaction's rate of progress vector.

It is initialized to one.

Definition at line 925 of file Kinetics.h.

## ◆ m_reactions

 std::vector > m_reactions
protected

Vector of Reaction objects represented by this Kinetics manager.

Definition at line 928 of file Kinetics.h.

## ◆ m_thermo

 std::vector m_thermo
protected

m_thermo is a vector of pointers to ThermoPhase objects that are involved with this kinetics operator

For homogeneous kinetics applications, this vector will only have one entry. For interfacial reactions, this vector will consist of multiple entries; some of them will be surface phases, and the other ones will be bulk phases. The order that the objects are listed determines the order in which the species comprising each phase are listed in the source term vector, originating from the reaction mechanism.

Note that this kinetics object doesn't own these ThermoPhase objects and is not responsible for creating or deleting them.

Definition at line 943 of file Kinetics.h.

## ◆ m_start

 std::vector m_start
protected

m_start is a vector of integers specifying the beginning position for the species vector for the n'th phase in the kinetics class.

Definition at line 949 of file Kinetics.h.

## ◆ m_phaseindex

 std::map m_phaseindex
protected

Mapping of the phase id, i.e., the id attribute in the XML phase element to the position of the phase within the kinetics object.

Positions start with the value of 1. The member function, phaseIndex() decrements by one before returning the index value, so that missing phases return -1.

Definition at line 957 of file Kinetics.h.

Referenced by Kinetics::addPhase(), Kinetics::operator=(), and Kinetics::phaseIndex().

## ◆ m_surfphase

 size_t m_surfphase
protected

Index in the list of phases of the one surface phase.

Definition at line 960 of file Kinetics.h.

Referenced by Kinetics::addPhase(), Kinetics::operator=(), and Kinetics::surfacePhaseIndex().

## ◆ m_rxnphase

 size_t m_rxnphase
protected

Phase Index where reactions are assumed to be taking place.

We calculate this by assuming that the phase with the lowest dimensionality is the phase where reactions are taking place.

Definition at line 967 of file Kinetics.h.

Referenced by Kinetics::addPhase(), Kinetics::operator=(), and Kinetics::reactionPhaseIndex().

## ◆ m_mindim

 size_t m_mindim
protected

number of spatial dimensions of lowest-dimensional phase.

Definition at line 970 of file Kinetics.h.

## ◆ m_rfn

 vector_fp m_rfn
protected

Forward rate constant for each reaction.

Definition at line 973 of file Kinetics.h.

## ◆ m_rkcn

 vector_fp m_rkcn
protected

Reciprocal of the equilibrium constant in concentration units.

Definition at line 976 of file Kinetics.h.

## ◆ m_ropf

 vector_fp m_ropf
protected

Forward rate-of-progress for each reaction.

Definition at line 979 of file Kinetics.h.

## ◆ m_ropr

 vector_fp m_ropr
protected

Reverse rate-of-progress for each reaction.

Definition at line 982 of file Kinetics.h.

## ◆ m_ropnet

 vector_fp m_ropnet
protected

Net rate-of-progress for each reaction.

Definition at line 985 of file Kinetics.h.

## ◆ m_skipUndeclaredSpecies

 bool m_skipUndeclaredSpecies
protected

## ◆ m_skipUndeclaredThirdBodies

 bool m_skipUndeclaredThirdBodies
protected